[bioontology-support] [BioPortal] Feedback from callahantiff

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[bioontology-support] [BioPortal] Feedback from callahantiff

support

Name: callahantiff

Email: [hidden email]

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMESH%3Fp%3Dnotes


Feedback:

Hello-

I am trying to access MESH via the api and while I get a 200 response, there is no data returned. I also tried to download full ontology and the download also fails. I was successful when trying the same commands on different ontologies, which makes me think there might be something wrong with MESH.

Please help and thank you in advance for your assistance! :D

-Tiffany Callahan
[hidden email]


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bioontology-support mailing list
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Re: [bioontology-support] [BioPortal] Feedback from callahantiff

Michael Dorf
Hi Tiffany,

Thank you for contacting us.  There may have been a temporary caching issue on our end that caused an empty result to be returned when you accessed it. I’ve just tried it now, and all MESH endpoints return results. Please let me know if the problem still persists for you.


Thank you,

----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
[hidden email]
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On Dec 2, 2020, at 6:51 PM, [hidden email] wrote:

Name: callahantiff

[hidden email]

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMESH%3Fp%3Dnotes


Feedback:

Hello-

I am trying to access MESH via the api and while I get a 200 response, there is no data returned. I also tried to download full ontology and the download also fails. I was successful when trying the same commands on different ontologies, which makes me think there might be something wrong with MESH.

Please help and thank you in advance for your assistance! :D

-Tiffany Callahan
[hidden email]


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] [BioPortal] Feedback from callahantiff

Tiffany Callahan

Hi Michael-

 

Thank you so much for your help! I did try again early this morning and found that it was working.

 

I hope it is OK that I ask a separate question in this email. I am currently running some Python code to query the BioPortal API to retrieve all MESH-CHEBI mappings. I am sleeping between processing each page as there are a lot of results, but it seems that I may be hitting the API too much. I have had the connection closed after processing ~2200 pages of results. I am wondering if there is a different approach that you prefer I use to avoid getting kicked off while also respecting the resource (I know I am not the only person who wants to use this awesome resource and I am happy to share 😃)? Alternatively, is there a more efficient way to obtain these mappings that you might recommend? Right now, using the API-based approach, I estimate it will take over 3 days to process all of the output (assuming it can run continuously).

 

Thank you again for your help and advice, I really appreciate it!

 

 

-Tiffany

 

From: Michael Dorf <[hidden email]>
Date: Thursday, December 3, 2020 at 16:08
To: "[hidden email]" <[hidden email]>
Cc: Tiffany Callahan <[hidden email]>
Subject: Re: [bioontology-support] [BioPortal] Feedback from callahantiff

 

Hi Tiffany,

 

Thank you for contacting us.  There may have been a temporary caching issue on our end that caused an empty result to be returned when you accessed it. I’ve just tried it now, and all MESH endpoints return results. Please let me know if the problem still persists for you.

 

 

Thank you,

 

----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
[hidden email]
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------



On Dec 2, 2020, at 6:51 PM, [hidden email] wrote:

 

Name: callahantiff

[hidden email]

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMESH%3Fp%3Dnotes


Feedback:

Hello-

I am trying to access MESH via the api and while I get a 200 response, there is no data returned. I also tried to download full ontology and the download also fails. I was successful when trying the same commands on different ontologies, which makes me think there might be something wrong with MESH.

Please help and thank you in advance for your assistance! :D

-Tiffany Callahan
[hidden email]

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] [BioPortal] Feedback from callahantiff

Michael Dorf
Hi Tiffany,

I apologize for the late reply. Except those that are specifically created by users, the majority of the mappings in our system are the lexical mappings generated on the fly using the “LOOM” algorithm (more info on this here: https://www.bioontology.org/wiki/BioPortal_Mappings). These aren’t stored anywhere but rather materialized “live” using the built-in algorithm. Unfortunately, REST service is the only reliable way to get these. Have you managed to complete the run of your script?

Thank you,

Michael



On Dec 3, 2020, at 8:53 PM, Tiffany Callahan <[hidden email]> wrote:

Hi Michael-
 
Thank you so much for your help! I did try again early this morning and found that it was working.
 
I hope it is OK that I ask a separate question in this email. I am currently running some Python code to query the BioPortal API to retrieve all MESH-CHEBI mappings. I am sleeping between processing each page as there are a lot of results, but it seems that I may be hitting the API too much. I have had the connection closed after processing ~2200 pages of results. I am wondering if there is a different approach that you prefer I use to avoid getting kicked off while also respecting the resource (I know I am not the only person who wants to use this awesome resource and I am happy to share 😃)? Alternatively, is there a more efficient way to obtain these mappings that you might recommend? Right now, using the API-based approach, I estimate it will take over 3 days to process all of the output (assuming it can run continuously).
 
Thank you again for your help and advice, I really appreciate it!
 
 
-Tiffany
 
From: Michael Dorf <[hidden email]>
Date: Thursday, December 3, 2020 at 16:08
To: "[hidden email]" <[hidden email]>
Cc: Tiffany Callahan <[hidden email]>
Subject: Re: [bioontology-support] [BioPortal] Feedback from callahantiff
 
Hi Tiffany, 
 
Thank you for contacting us.  There may have been a temporary caching issue on our end that caused an empty result to be returned when you accessed it. I’ve just tried it now, and all MESH endpoints return results. Please let me know if the problem still persists for you.
 
 
Thank you,
 
----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
[hidden email]
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------


On Dec 2, 2020, at 6:51 PM, [hidden email] wrote:
 
Name: callahantiff
Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMESH%3Fp%3Dnotes

Feedback:
Hello-
I am trying to access MESH via the api and while I get a 200 response, there is no data returned. I also tried to download full ontology and the download also fails. I was successful when trying the same commands on different ontologies, which makes me think there might be something wrong with MESH.
Please help and thank you in advance for your assistance! :D
-Tiffany Callahan 
[hidden email]
 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] [BioPortal] Feedback from callahantiff

Tiffany Callahan

Hi Michael-

 

Thanks so much for your response and help. I have successfully completed my run. I am hoping to integrate this code into a monthly deployment build. Do you think that assuming I don’t ping the API at too quick of an interval this would be OK?

 

 

-Tiffany

 

From: Michael Dorf <[hidden email]>
Date: Tuesday, December 15, 2020 at 11:29
To: Tiffany Callahan <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [bioontology-support] [BioPortal] Feedback from callahantiff

 

Hi Tiffany,

 

I apologize for the late reply. Except those that are specifically created by users, the majority of the mappings in our system are the lexical mappings generated on the fly using the “LOOM” algorithm (more info on this here: https://www.bioontology.org/wiki/BioPortal_Mappings). These aren’t stored anywhere but rather materialized “live” using the built-in algorithm. Unfortunately, REST service is the only reliable way to get these. Have you managed to complete the run of your script?

 

Thank you,

 

Michael

 

 



On Dec 3, 2020, at 8:53 PM, Tiffany Callahan <[hidden email]> wrote:

 

Hi Michael-

 

Thank you so much for your help! I did try again early this morning and found that it was working.

 

I hope it is OK that I ask a separate question in this email. I am currently running some Python code to query the BioPortal API to retrieve all MESH-CHEBI mappings. I am sleeping between processing each page as there are a lot of results, but it seems that I may be hitting the API too much. I have had the connection closed after processing ~2200 pages of results. I am wondering if there is a different approach that you prefer I use to avoid getting kicked off while also respecting the resource (I know I am not the only person who wants to use this awesome resource and I am happy to share 😃)? Alternatively, is there a more efficient way to obtain these mappings that you might recommend? Right now, using the API-based approach, I estimate it will take over 3 days to process all of the output (assuming it can run continuously).

 

Thank you again for your help and advice, I really appreciate it!

 

 

-Tiffany

 

From: Michael Dorf <[hidden email]>
Date: Thursday, December 3, 2020 at 16:08
To: "[hidden email]" <[hidden email]>
Cc: Tiffany Callahan <[hidden email]>
Subject: Re: [bioontology-support] [BioPortal] Feedback from callahantiff

 

Hi Tiffany, 

 

Thank you for contacting us.  There may have been a temporary caching issue on our end that caused an empty result to be returned when you accessed it. I’ve just tried it now, and all MESH endpoints return results. Please let me know if the problem still persists for you.

 

 

Thank you,

 

----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
[hidden email]
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

 

On Dec 2, 2020, at 6:51 PM, [hidden email] wrote:

 

Name: callahantiff

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMESH%3Fp%3Dnotes


Feedback:

Hello-

I am trying to access MESH via the api and while I get a 200 response, there is no data returned. I also tried to download full ontology and the download also fails. I was successful when trying the same commands on different ontologies, which makes me think there might be something wrong with MESH.

Please help and thank you in advance for your assistance! :D

-Tiffany Callahan 
[hidden email]

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support